| T0819 |
| ID: | 1402693020 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 373 (340) | ||
| Sequences: | 44268 (30478.1) | ||
| Seq/Len: | 130.200 | ||
| Nf(neff/√len): | 1652.9 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 130.200).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 56_R | 60_G | 3.837 | 1.00 |
| 288_R | 357_D | 3.822 | 1.00 |
| 330_H | 365_E | 3.689 | 1.00 |
| 76_A | 270_A | 3.576 | 1.00 |
| 149_L | 187_E | 3.089 | 1.00 |
| 292_I | 360_A | 2.955 | 1.00 |
| 182_A | 186_P | 2.814 | 1.00 |
| 325_R | 329_D | 2.672 | 1.00 |
| 53_L | 57_Q | 2.627 | 1.00 |
| 288_R | 353_D | 2.571 | 1.00 |
| 267_A | 270_A | 2.536 | 1.00 |
| 91_G | 97_L | 2.506 | 1.00 |
| 49_P | 53_L | 2.459 | 1.00 |
| 145_L | 180_A | 2.436 | 1.00 |
| 358_L | 362_A | 2.301 | 1.00 |
| 111_P | 132_R | 2.231 | 1.00 |
| 283_A | 287_Q | 2.229 | 1.00 |
| 174_P | 177_R | 2.201 | 1.00 |
| 292_I | 295_D | 2.198 | 1.00 |
| 111_P | 134_V | 2.171 | 1.00 |
| 284_N | 353_D | 2.171 | 1.00 |
| 240_S | 245_A | 2.156 | 1.00 |
| 281_K | 285_S | 2.125 | 1.00 |
| 288_R | 292_I | 2.114 | 1.00 |
| 110_A | 158_P | 2.098 | 1.00 |
| 287_Q | 291_R | 2.081 | 1.00 |
| 76_A | 266_I | 2.011 | 1.00 |
| 111_P | 153_G | 2.011 | 1.00 |
| 50_S | 267_A | 2.007 | 1.00 |
| 52_L | 56_R | 1.984 | 1.00 |
| 147_G | 150_A | 1.957 | 1.00 |
| 299_A | 311_D | 1.953 | 1.00 |
| 111_P | 156_N | 1.953 | 1.00 |
| 111_P | 157_A | 1.938 | 1.00 |
| 292_I | 357_D | 1.924 | 1.00 |
| 38_I | 359_L | 1.918 | 1.00 |
| 147_G | 151_A | 1.918 | 1.00 |
| 137_P | 147_G | 1.886 | 1.00 |
| 75_Q | 79_R | 1.873 | 1.00 |
| 180_A | 183_Q | 1.856 | 1.00 |
| 159_L | 192_V | 1.844 | 1.00 |
| 72_D | 266_I | 1.795 | 1.00 |
| 149_L | 184_A | 1.784 | 1.00 |
| 179_V | 183_Q | 1.783 | 1.00 |
| 175_A | 179_V | 1.782 | 1.00 |
| 116_L | 137_P | 1.777 | 1.00 |
| 183_Q | 187_E | 1.770 | 1.00 |
| 145_L | 184_A | 1.767 | 1.00 |
| 87_N | 242_P | 1.732 | 1.00 |
| 291_R | 295_D | 1.710 | 1.00 |
| 352_P | 355_E | 1.707 | 1.00 |
| 149_L | 153_G | 1.703 | 1.00 |
| 50_S | 271_D | 1.697 | 1.00 |
| 185_L | 191_L | 1.695 | 1.00 |
| 277_E | 280_L | 1.677 | 1.00 |
| 185_L | 189_T | 1.674 | 1.00 |
| 290_G | 294_A | 1.649 | 1.00 |
| 235_I | 265_A | 1.630 | 1.00 |
| 325_R | 330_H | 1.627 | 1.00 |
| 332_I | 362_A | 1.624 | 1.00 |
| 258_S | 261_G | 1.620 | 1.00 |
| 106_V | 131_G | 1.609 | 1.00 |
| 326_L | 334_I | 1.593 | 1.00 |
| 222_R | 237_Y | 1.581 | 1.00 |
| 86_A | 242_P | 1.560 | 1.00 |
| 144_D | 147_G | 1.552 | 1.00 |
| 292_I | 361_A | 1.541 | 1.00 |
| 57_Q | 61_D | 1.537 | 1.00 |
| 358_L | 361_A | 1.533 | 1.00 |
| 48_A | 271_D | 1.515 | 1.00 |
| 330_H | 362_A | 1.512 | 1.00 |
| 149_L | 180_A | 1.511 | 1.00 |
| 348_I | 359_L | 1.509 | 1.00 |
| 53_L | 56_R | 1.504 | 1.00 |
| 101_I | 219_I | 1.498 | 1.00 |
| 160_V | 185_L | 1.490 | 1.00 |
| 318_Y | 321_A | 1.488 | 1.00 |
| 54_A | 267_A | 1.475 | 1.00 |
| 146_E | 150_A | 1.465 | 1.00 |
| 325_R | 366_V | 1.465 | 1.00 |
| 292_I | 296_S | 1.463 | 1.00 |
| 113_V | 157_A | 1.452 | 1.00 |
| 72_D | 270_A | 1.449 | 1.00 |
| 55_I | 264_A | 1.444 | 1.00 |
| 280_L | 284_N | 1.442 | 1.00 |
| 292_I | 364_P | 1.440 | 1.00 |
| 55_I | 59_A | 1.440 | 1.00 |
| 296_S | 364_P | 1.436 | 1.00 |
| 76_A | 79_R | 1.423 | 1.00 |
| 176_E | 179_V | 1.413 | 1.00 |
| 161_Y | 192_V | 1.411 | 1.00 |
| 321_A | 325_R | 1.408 | 1.00 |
| 361_A | 365_E | 1.406 | 0.99 |
| 310_V | 348_I | 1.394 | 0.99 |
| 99_G | 103_R | 1.384 | 0.99 |
| 75_Q | 85_P | 1.378 | 0.99 |
| 92_E | 96_G | 1.378 | 0.99 |
| 52_L | 60_G | 1.376 | 0.99 |
| 160_V | 189_T | 1.372 | 0.99 |
| 88_I | 239_L | 1.357 | 0.99 |
| 94_I | 221_A | 1.355 | 0.99 |
| 267_A | 271_D | 1.352 | 0.99 |
| 146_E | 149_L | 1.345 | 0.99 |
| 192_V | 221_A | 1.343 | 0.99 |
| 152_V | 184_A | 1.343 | 0.99 |
| 266_I | 270_A | 1.319 | 0.99 |
| 195_E | 220_R | 1.317 | 0.99 |
| 290_G | 308_V | 1.315 | 0.99 |
| 182_A | 191_L | 1.306 | 0.99 |
| 281_K | 284_N | 1.298 | 0.99 |
| 146_E | 180_A | 1.296 | 0.99 |
| 332_I | 359_L | 1.292 | 0.99 |
| 77_L | 237_Y | 1.292 | 0.99 |
| 152_V | 189_T | 1.291 | 0.99 |
| 285_S | 353_D | 1.277 | 0.99 |
| 116_L | 135_T | 1.272 | 0.99 |
| 224_F | 265_A | 1.258 | 0.99 |
| 32_R | 331_G | 1.251 | 0.99 |
| 353_D | 357_D | 1.249 | 0.99 |
| 286_R | 290_G | 1.249 | 0.99 |
| 126_V | 131_G | 1.241 | 0.98 |
| 101_I | 192_V | 1.240 | 0.98 |
| 177_R | 180_A | 1.228 | 0.98 |
| 364_P | 368_R | 1.226 | 0.98 |
| 359_L | 362_A | 1.211 | 0.98 |
| 242_P | 246_Q | 1.203 | 0.98 |
| 81_L | 239_L | 1.200 | 0.98 |
| 291_R | 294_A | 1.195 | 0.98 |
| 325_R | 369_S | 1.192 | 0.98 |
| 52_L | 59_A | 1.184 | 0.98 |
| 71_H | 75_Q | 1.182 | 0.98 |
| 164_N | 198_C | 1.179 | 0.98 |
| 153_G | 157_A | 1.169 | 0.97 |
| 110_A | 156_N | 1.169 | 0.97 |
| 330_H | 369_S | 1.162 | 0.97 |
| 91_G | 236_G | 1.159 | 0.97 |
| 50_S | 275_L | 1.152 | 0.97 |
| 285_S | 356_M | 1.141 | 0.97 |
| 136_V | 151_A | 1.136 | 0.97 |
| 285_S | 288_R | 1.133 | 0.97 |
| 289_I | 292_I | 1.129 | 0.97 |
| 134_V | 151_A | 1.121 | 0.97 |
| 323_V | 334_I | 1.113 | 0.96 |
| 196_A | 223_T | 1.113 | 0.96 |
| 357_D | 361_A | 1.110 | 0.96 |
| 142_R | 177_R | 1.105 | 0.96 |
| 188_T | 217_N | 1.099 | 0.96 |
| 113_V | 151_A | 1.092 | 0.96 |
| 295_D | 364_P | 1.089 | 0.96 |
| 176_E | 180_A | 1.089 | 0.96 |
| 139_A | 177_R | 1.088 | 0.96 |
| 183_Q | 186_P | 1.088 | 0.96 |
| 84_S | 242_P | 1.084 | 0.96 |
| 162_L | 178_V | 1.083 | 0.96 |
| 294_A | 300_P | 1.081 | 0.95 |
| 150_A | 154_R | 1.079 | 0.95 |
| 73_L | 266_I | 1.074 | 0.95 |
| 280_L | 283_A | 1.074 | 0.95 |
| 102_V | 161_Y | 1.070 | 0.95 |
| 184_A | 189_T | 1.069 | 0.95 |
| 324_D | 329_D | 1.068 | 0.95 |
| 49_P | 52_L | 1.067 | 0.95 |
| 326_L | 363_L | 1.058 | 0.95 |
| 355_E | 358_L | 1.057 | 0.95 |
| 57_Q | 60_G | 1.054 | 0.95 |
| 321_A | 324_D | 1.052 | 0.95 |
| 284_N | 288_R | 1.047 | 0.94 |
| 98_L | 192_V | 1.043 | 0.94 |
| 152_V | 157_A | 1.042 | 0.94 |
| 112_V | 159_L | 1.037 | 0.94 |
| 323_V | 336_M | 1.036 | 0.94 |
| 83_T | 239_L | 1.031 | 0.94 |
| 334_I | 346_I | 1.030 | 0.94 |
| 153_G | 156_N | 1.027 | 0.94 |
| 326_L | 362_A | 1.025 | 0.93 |
| 77_L | 90_I | 1.018 | 0.93 |
| 112_V | 126_V | 1.012 | 0.93 |
| 78_A | 85_P | 1.011 | 0.93 |
| 359_L | 363_L | 1.010 | 0.93 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3getA | 2 | 0.9517 | 100 | 0.297 | Contact Map |
| 3ffhA | 2 | 0.9383 | 100 | 0.301 | Contact Map |
| 3ly1A | 4 | 0.9357 | 100 | 0.322 | Contact Map |
| 3hdoA | 2 | 0.9223 | 100 | 0.325 | Contact Map |
| 3eucA | 2 | 0.933 | 100 | 0.328 | Contact Map |
| 1fg7A | 1 | 0.9303 | 100 | 0.332 | Contact Map |
| 3ftbA | 4 | 0.8767 | 100 | 0.334 | Contact Map |
| 2o1bA | 1 | 0.9464 | 100 | 0.335 | Contact Map |
| 3b46A | 2 | 0.9705 | 100 | 0.336 | Contact Map |
| 1b5pA | 2 | 0.9571 | 100 | 0.338 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)